The change comes after the healthy food star rating website was published and then quickly taken down at the insistence of federal Assistant Health Minister Fiona Nash and her chief of staff.

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In an email obtained by Fairfax Media, Kathy Dennis, the assistant secretary in the Healthy Living and Food Policy branch of the Department of Health, said she would no longer be in charge of the healthy star ratings, which is a system for food manufacturers to label their product packaging voluntarily with easy-to-understand health information.

"I am writing to provide you with updated information about arrangements for the Front-of-Pack Labelling Secretariat, following a restructure within the Department of Health," Ms Dennis writes. She states that she will continue to be in charge of all other food matters beside the healthy food ratings, on which she has worked for the past two years.

A screen grab of the website before it was discontinued.

"I look forward to continuing to work with you on all other food matters," she says.

Fairfax Media understands that the move is unusual, as it will result in the director of the healthy star program now reporting to someone less senior than Ms Dennis, despite Ms Dennis still retaining control of other food issues.

Public health and consumer groups are furious that the site has been taken offline after two years in development, and have accused the government of bowing to the interests of the junk food industry.

Senator Nash has been under fire in Parliament this week after she revealed that she and her chief of staff, Alastair Furnival, had intervened to take down the healthy star website, despite it being developed as part of a state and territory food ministers’ forum.

Fairfax Media understands Senator Nash chairs the forum, but does not have executive decision-making control over it, with programs developed on a consensus basis.

In a late-night statement to the senate on Tuesday, Senator Nash revealed Mr Furnival had a shareholding in a company that lobbies for the soft-drink and confectionary industry.

Earlier that day she had told Parliament there was "no connection whatsoever" between her chief of staff and the company, Australian Public Affairs (APA).

Labor has accused Senator Nash of making misleading statements, and of violating rules that insist ministers and their staff must disclose any real or apparent conflict of interest, and divest themselves of any interests in private companies involved in the area of their ministerial responsibilities.

"I am genuinely disappointed to have to say that these revelations represent serious negligence in her conduct of her ministerial responsibilities," he told Parliament on Wednesday.

Senator Nash had said she was "fully aware" of the rules around disclosure of conflict of interest, and that none existed despite Mr Furnival’s shareholding in APA.

"My chief of staff took proper and appropriate steps to prevent any conflict of interest with the private business of APA and by withdrawing from any work from APA, and on that basis there was no conflict of interest," she said.

She said Mr Furnival had not earned any money from his shareholding, and that his wife, Tracey Cain, who is the sole director and secretary of the company, had undertaken not to conduct any lobbying in the health area. In a statement, Ms Cain said she had not made any representations on behalf of food industry clients since September.

"It would be disappointing if we had reached a point where people were disqualified from public service as a result of expertise that they, or for that matter, their wives, had gained in the private sector," Ms Cain said.

A spokeswoman for the federal Department of Health said there were "all sorts of reporting arrangements" within the department.

"In this instance it was decided that, as the ministerial food standards forum is a joint Commonwealth and State and Territory committee, that the secretariat should report to a separate officer, other than the Commonwealth officer responsible for food issues," she said.